A key question in evolutionary biology is how molecular variation relates to phenotypic diversity. Arabidopsis FLOWERING LOCUS C (FLC) plays a key role in controlling vernalization—the acceleration of flowering by prolonged cold. Li et al. identify five functionally distinct FLC haplotypes, defined by noncoding sequence variation, which vary in FLC expression level and silencing. Allelic heterogeneity at this single locus accounts for a large proportion of variation in Arabidopsis vernalization. This study advances our understanding of adaptation and provides a new paradigm for analysis of complex traits.